Haptically enable interactive virtual assembly training system development and evaluation

Virtual training systems are attracting paramount attention from the manufacturing industries due to their potential advantages over the conventional training practices. Significant cost savings can be realized due to the shorter times for the development of different training-scenarios as well as reuse of existing designed engineering (math) models. In addition, use of computer based virtual reality (VR) training systems can shorten the time span from computer aided product design to commercial production due to non-reliance on the hardware parts for training. Within the aforementioned conceptual framework, a haptically enabled interactive and immersive virtual reality (HIVEx) system is presented. Unlike existing VR systems, the presented idea tries to imitate real physical training scenarios by providing comprehensive user interaction, constrained within the physical limitations of the real world. These physical constrains are imposed by the haptics devices in the virtual environment. As a result, in contrast to the existing VR systems that are capable of providing knowledge generally about assembly sequences only, the proposed system helps in cognitive learning and procedural skill development as well, due to its high physically interactive nature.

Evolution of JAK-STAT pathway components : mechanisms and role in immune system development

Background
Lying downstream of a myriad of cytokine receptors, the Janus kinase (JAK) – Signal transducer and activator of transcription (STAT) pathway is pivotal for the development and function of the immune system, with additional important roles in other biological systems. To gain further insight into immune system evolution, we have performed a comprehensive bioinformatic analysis of the JAK-STAT pathway components, including the key negative regulators of this pathway, the SH2-domain containing tyrosine phosphatase (SHP), Protein inhibitors against Stats (PIAS), and Suppressor of cytokine signaling (SOCS) proteins across a diverse range of organisms.

Results
Our analysis has demonstrated significant expansion of JAK-STAT pathway components co-incident with the emergence of adaptive immunity, with whole genome duplication being the principal mechanism for generating this additional diversity. In contrast, expansion of upstream cytokine receptors appears to be a pivotal driver for the differential diversification of specific pathway components.

Conclusion
Diversification of JAK-STAT pathway components during early vertebrate development occurred concurrently with a major expansion of upstream cytokine receptors and two rounds of whole genome duplications. This produced an intricate cell-cell communication system that has made a significant contribution to the evolution of the immune system, particularly the emergence of adaptive immunity.

Functional system maps as boundary objects in complex system development

A trend towards the provision of product-service packaging and the proliferation of service businesses introduces both tangible and intangible elements into system design. In this paper, we consider the utility of hierarchical system models as a way of flexibly combining such elements by focusing on requisite functionality. Four cases illustrate how the same approach may be used to clarify the requirements of business or socio-technical systems during system development, operation or reengineering stages. It is suggested that a suitable loosely coupled model has significant utility as a 'boundary object' - a term first coined in the study of museum artefacts. Discussion of such objects requires the use of imagination, which may support innovative system design and development. It is suggested that a well-crafted model has multiple uses - as a foundation for system development, in combining traditional and agile project management strategies and in providing a framework to facilitate the capture and organisation of project knowledge.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Sustainable Air Traffic Management System Development Methodology

As it is defined in ATM 2000+ Strategy (Eurocontrol 2001), the mission of the Air Traffic Management (ATM) System is: “For all the phases of a flight, the ATM system should facilitate a safe, efficient, and expedite traffic flow, through the provision of adaptable ATM services that can be dimensioned in relation to the requirements of all the users and areas of the European air space. The ATM services should comply with the demand, be compatible, operate under uniform principles, respect the environment and satisfy the national security requirements.” The objective of this paper is to present a methodology designed to evaluate the status of the ATM system in terms of the relationship between the offered capacity and traffic demand, identifying weakness areas and proposing solutions. The first part of the methodology relates to the characterization and evaluation of the current system, while a second part proposes an approach to analyze the possible development limit. As part of the work, general criteria are established to define the framework in which the analysis and diagnostic methodology presented is placed. They are: the use of Air Traffic Control (ATC) sectors as analysis unit, the presence of network effects, the tactical focus, the relative character of the analysis, objectivity and a high level assessment that allows assumptions on the human and Communications, Navigation and Surveillance (CNS) elements, considered as the typical high density air traffic resources. The steps followed by the methodology start with the definition of indicators and metrics, like the nominal criticality or the nominal efficiency of a sector; scenario characterization where the necessary data is collected; network effects analysis to study the relations among the constitutive elements of the ATC system; diagnostic by means of the “System Status Diagram”; analytical study of the ATC system development limit; and finally, formulation of conclusions and proposal for improvement. This methodology was employed by Aena (Spanish Airports Manager and Air Navigation Service Provider) and INECO (Spanish Transport Engineering Company) in the analysis of the Spanish ATM System in the frame of the Spanish airspace capacity sustainability program, although it could be applied elsewhere.

Fibroblast growth factor (FGF) homologous factors: new members of the FGF family implicated in nervous system development.

Four new members of the fibroblast growth factor (FGF) family, referred to as fibroblast growth factor homologous factors (FHFs), have been identified by a combination of random cDNA sequencing, data base searches, and degenerate PCR. Pairwise comparisons between the four FHFs show between 58% and 71% amino acid sequence identity, but each FHF shows less than 30% identity when compared with other FGFs. Like FGF-1 (acidic FGF) and FGF-2 (basic FGF), the FHFs lack a classical signal sequence and contain clusters of basic residues that can act as nuclear localization signals. In transiently transfected 293 cells FHF-1 accumulates in the nucleus and is not secreted. Each FHF is expressed in the developing and adult nervous systems, suggesting a role for this branch of the FGF family in nervous system development and function.

Emergence of order in visual system development.

Neural connections in the adult central nervous system are highly precise. In the visual system, retinal ganglion cells send their axons to target neurons in the lateral geniculate nucleus (LGN) in such a way that axons originating from the two eyes terminate in adjacent but nonoverlapping eye-specific layers. During development, however, inputs from the two eyes are intermixed, and the adult pattern emerges gradually as axons from the two eyes sort out to form the layers. Experiments indicate that the sorting-out process, even though it occurs in utero in higher mammals and always before vision, requires retinal ganglion cell signaling; blocking retinal ganglion cell action potentials with tetrodotoxin prevents the formation of the layers. These action potentials are endogenously generated by the ganglion cells, which fire spontaneously and synchronously with each other, generating "waves" of activity that travel across the retina. Calcium imaging of the retina shows that the ganglion cells undergo correlated calcium bursting to generate the waves and that amacrine cells also participate in the correlated activity patterns. Physiological recordings from LGN neurons in vitro indicate that the quasiperiodic activity generated by the retinal ganglion cells is transmitted across the synapse between ganglion cells to drive target LGN neurons. These observations suggest that (i) a neural circuit within the immature retina is responsible for generating specific spatiotemporal patterns of neural activity; (ii) spontaneous activity generated in the retina is propagated across central synapses; and (iii) even before the photoreceptors are present, nerve cell function is essential for correct wiring of the visual system during early development. Since spontaneously generated activity is known to be present elsewhere in the developing CNS, this process of activity-dependent wiring could be used throughout the nervous system to help refine early sets of neural connections into their highly precise adult patterns.

Down syndrome-critical region contains a gene homologous to Drosophila sim expressed during rat and human central nervous system development.

Many features of Down syndrome might result from the overdosage of only a few genes located in a critical region of chromosome 21. To search for these genes, cosmids mapping in this region were isolated and used for trapping exons. One of the trapped exons obtained has a sequence very similar to part of the Drosophila single-minded (sim) gene, a master regulator of the early development of the fly central nervous system midline. Mapping data indicated that this exonic sequence is only present in the Down syndrome-critical region in the human genome. Hybridization of this exonic sequence with human fetal kidney poly(A)+ RNA revealed two transcripts of 6 and 4.3 kb. In situ hybridization of a probe derived from this exon with human and rat fetuses showed that the corresponding gene is expressed during early fetal life in the central nervous system and in other tissues, including the facial, skull, palate, and vertebra primordia. The expression pattern of this gene suggests that it might be involved in the pathogenesis of some of the morphological features and brain anomalies observed in Down syndrome.

Intraoperative image-guided navigation system: development and applicability in 65 patients undergoing liver surgery

Background Image-guided systems have recently been introduced for their application in liver surgery.We aimed to identify and propose suitable indications for image-guided navigation systems in the domain of open oncologic liver surgery and,more specifically, in the setting of liver resection with and without microwave ablation. Method Retrospective analysis was conducted in patients undergoing liver resection with and without microwave ablation using an intraoperative image-guided stereotactic system during three stages of technological development (accuracy: 8.4 ± 4.4 mm in phase I and 8.4 ± 6.5 mm in phase II versus 4.5 ± 3.6 mm in phase III). It was evaluated, in which indications image-guided surgery was used according to the different stages of technical development. Results Between 2009 and 2013, 65 patients underwent image-guided surgical treatment, resection alone (n=38), ablation alone (n =11), or a combination thereof (n =16). With increasing accuracy of the system, image guidance was progressively used for atypical resections and combined microwave ablation and resection instead of formal liver resection (p<0.0001). Conclusion Clinical application of image guidance is feasible, while its efficacy is subject to accuracy. The concept of image guidance has been shown to be increasingly efficient for selected indications in liver surgery. While accuracy of available technology is increasing pertaining to technological advancements, more and more previously untreatable scenarios such as multiple small, bilobar lesions and so-called vanishing lesions come within reach.